메뉴 건너뛰기




Volumn 60, Issue 2, 2015, Pages 256-267

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

Author keywords

[No Author keywords available]

Indexed keywords

EXONUCLEASE; HISTONE; MUTANT PROTEIN; POLYADENYLIC ACID; PROTEIN; PROTEIN XRN2; RNA POLYMERASE II; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG; EXORIBONUCLEASE; MESSENGER RNA; XRN2 PROTEIN, HUMAN;

EID: 84944887484     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2015.09.026     Document Type: Article
Times cited : (160)

References (62)
  • 2
    • 84862229469 scopus 로고    scopus 로고
    • RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts
    • Anamika K., Gyenis À., Poidevin L., Poch O., Tora L. RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts. PLoS ONE 2012, 7:e38769.
    • (2012) PLoS ONE , vol.7 , pp. e38769
    • Anamika, K.1    Gyenis, À.2    Poidevin, L.3    Poch, O.4    Tora, L.5
  • 3
    • 84872183608 scopus 로고    scopus 로고
    • How to stop: the mysterious links among RNA polymerase II occupancy 3' of genes, mRNA 3' processing and termination
    • Anamika K., Gyenis À., Tora L. How to stop: the mysterious links among RNA polymerase II occupancy 3' of genes, mRNA 3' processing and termination. Transcription 2013, 4:7-12.
    • (2013) Transcription , vol.4 , pp. 7-12
    • Anamika, K.1    Gyenis, À.2    Tora, L.3
  • 4
    • 26844493853 scopus 로고    scopus 로고
    • Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II
    • Baillat D., Hakimi M.A., Näär A.M., Shilatifard A., Cooch N., Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 2005, 123:265-276.
    • (2005) Cell , vol.123 , pp. 265-276
    • Baillat, D.1    Hakimi, M.A.2    Näär, A.M.3    Shilatifard, A.4    Cooch, N.5    Shiekhattar, R.6
  • 7
    • 67650340215 scopus 로고    scopus 로고
    • A novel tandem reporter quantifies RNA polymerase II termination in mammalian cells
    • Banerjee A., Sammarco M.C., Ditch S., Wang J., Grabczyk E. A novel tandem reporter quantifies RNA polymerase II termination in mammalian cells. PLoS ONE 2009, 4:e6193.
    • (2009) PLoS ONE , vol.4 , pp. e6193
    • Banerjee, A.1    Sammarco, M.C.2    Ditch, S.3    Wang, J.4    Grabczyk, E.5
  • 8
  • 11
    • 0023990221 scopus 로고
    • A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II
    • Connelly S., Manley J.L. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 1988, 2:440-452.
    • (1988) Genes Dev. , vol.2 , pp. 440-452
    • Connelly, S.1    Manley, J.L.2
  • 12
    • 84876842759 scopus 로고    scopus 로고
    • Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    • Danko C.G., Hah N., Luo X., Martins A.L., Core L., Lis J.T., Siepel A., Kraus W.L. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 2013, 50:212-222.
    • (2013) Mol. Cell , vol.50 , pp. 212-222
    • Danko, C.G.1    Hah, N.2    Luo, X.3    Martins, A.L.4    Core, L.5    Lis, J.T.6    Siepel, A.7    Kraus, W.L.8
  • 13
    • 84926304438 scopus 로고    scopus 로고
    • Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs
    • Dhir A., Dhir S., Proudfoot N.J., Jopling C.L. Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. Nat. Struct. Mol. Biol. 2015, 22:319-327.
    • (2015) Nat. Struct. Mol. Biol. , vol.22 , pp. 319-327
    • Dhir, A.1    Dhir, S.2    Proudfoot, N.J.3    Jopling, C.L.4
  • 14
    • 34247157802 scopus 로고    scopus 로고
    • Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism
    • Dominski Z. Nucleases of the metallo-beta-lactamase family and their role in DNA and RNA metabolism. Crit. Rev. Biochem. Mol. Biol. 2007, 42:67-93.
    • (2007) Crit. Rev. Biochem. Mol. Biol. , vol.42 , pp. 67-93
    • Dominski, Z.1
  • 15
    • 26244452759 scopus 로고    scopus 로고
    • The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing
    • Dominski Z., Yang X.C., Marzluff W.F. The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing. Cell 2005, 123:37-48.
    • (2005) Cell , vol.123 , pp. 37-48
    • Dominski, Z.1    Yang, X.C.2    Marzluff, W.F.3
  • 18
    • 84924356550 scopus 로고    scopus 로고
    • The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway
    • Fox M.J., Gao H., Smith-Kinnaman W.R., Liu Y., Mosley A.L. The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway. PLoS Genet. 2015, 11:e1004999.
    • (2015) PLoS Genet. , vol.11 , pp. e1004999
    • Fox, M.J.1    Gao, H.2    Smith-Kinnaman, W.R.3    Liu, Y.4    Mosley, A.L.5
  • 19
    • 84991566019 scopus 로고    scopus 로고
    • 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells
    • Fuchs G., Voichek Y., Benjamin S., Gilad S., Amit I., Oren M. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol. 2014, 15:R69.
    • (2014) Genome Biol. , vol.15 , pp. R69
    • Fuchs, G.1    Voichek, Y.2    Benjamin, S.3    Gilad, S.4    Amit, I.5    Oren, M.6
  • 20
    • 37849036555 scopus 로고    scopus 로고
    • RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes
    • Glover-Cutter K., Kim S., Espinosa J., Bentley D.L. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat. Struct. Mol. Biol. 2008, 15:71-78.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 71-78
    • Glover-Cutter, K.1    Kim, S.2    Espinosa, J.3    Bentley, D.L.4
  • 21
    • 33646556092 scopus 로고    scopus 로고
    • Pause sites promote transcriptional termination of mammalian RNA polymerase II
    • Gromak N., West S., Proudfoot N.J. Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol. Cell. Biol. 2006, 26:3986-3996.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 3986-3996
    • Gromak, N.1    West, S.2    Proudfoot, N.J.3
  • 22
    • 84864577725 scopus 로고    scopus 로고
    • Dynamic transitions in RNA polymerase II density profiles during transcription termination
    • Grosso A.R., de Almeida S.F., Braga J., Carmo-Fonseca M. Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome Res. 2012, 22:1447-1456.
    • (2012) Genome Res. , vol.22 , pp. 1447-1456
    • Grosso, A.R.1    de Almeida, S.F.2    Braga, J.3    Carmo-Fonseca, M.4
  • 23
    • 84872269907 scopus 로고    scopus 로고
    • Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination
    • Hazelbaker D.Z., Marquardt S., Wlotzka W., Buratowski S. Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination. Mol. Cell 2013, 49:55-66.
    • (2013) Mol. Cell , vol.49 , pp. 55-66
    • Hazelbaker, D.Z.1    Marquardt, S.2    Wlotzka, W.3    Buratowski, S.4
  • 24
    • 0026527507 scopus 로고
    • Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho
    • Jin D.J., Burgess R.R., Richardson J.P., Gross C.A. Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. Proc. Natl. Acad. Sci. USA 1992, 89:1453-1457.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 1453-1457
    • Jin, D.J.1    Burgess, R.R.2    Richardson, J.P.3    Gross, C.A.4
  • 25
    • 79951969817 scopus 로고    scopus 로고
    • Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay
    • Jinek M., Coyle S.M., Doudna J.A. Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol. Cell 2011, 41:600-608.
    • (2011) Mol. Cell , vol.41 , pp. 600-608
    • Jinek, M.1    Coyle, S.M.2    Doudna, J.A.3
  • 26
    • 34447550769 scopus 로고    scopus 로고
    • The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3' processing and transcription termination
    • Kaneko S., Rozenblatt-Rosen O., Meyerson M., Manley J.L. The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3' processing and transcription termination. Genes Dev. 2007, 21:1779-1789.
    • (2007) Genes Dev. , vol.21 , pp. 1779-1789
    • Kaneko, S.1    Rozenblatt-Rosen, O.2    Meyerson, M.3    Manley, J.L.4
  • 29
    • 26944459450 scopus 로고    scopus 로고
    • Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs
    • Kolev N.G., Steitz J.A. Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs. Genes Dev. 2005, 19:2583-2592.
    • (2005) Genes Dev. , vol.19 , pp. 2583-2592
    • Kolev, N.G.1    Steitz, J.A.2
  • 30
    • 79955475464 scopus 로고    scopus 로고
    • Unravelling the means to an end: RNA polymerase II transcription termination
    • Kuehner J.N., Pearson E.L., Moore C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat. Rev. Mol. Cell Biol. 2011, 12:283-294.
    • (2011) Nat. Rev. Mol. Cell Biol. , vol.12 , pp. 283-294
    • Kuehner, J.N.1    Pearson, E.L.2    Moore, C.3
  • 31
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 32
    • 79955407832 scopus 로고    scopus 로고
    • Real-time observation of transcription initiation and elongation on an endogenous yeast gene
    • Larson D.R., Zenklusen D., Wu B., Chao J.A., Singer R.H. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 2011, 332:475-478.
    • (2011) Science , vol.332 , pp. 475-478
    • Larson, D.R.1    Zenklusen, D.2    Wu, B.3    Chao, J.A.4    Singer, R.H.5
  • 34
    • 48949092575 scopus 로고    scopus 로고
    • A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation
    • Lian Z., Karpikov A., Lian J., Mahajan M.C., Hartman S., Gerstein M., Snyder M., Weissman S.M. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res. 2008, 18:1224-1237.
    • (2008) Genome Res. , vol.18 , pp. 1224-1237
    • Lian, Z.1    Karpikov, A.2    Lian, J.3    Mahajan, M.C.4    Hartman, S.5    Gerstein, M.6    Snyder, M.7    Weissman, S.M.8
  • 35
    • 0023478621 scopus 로고
    • A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene
    • Logan J., Falck-Pedersen E., Darnell J.E.J., Shenk T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc. Natl. Acad. Sci. USA 1987, 84:8306-8310.
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 8306-8310
    • Logan, J.1    Falck-Pedersen, E.2    Darnell, J.E.J.3    Shenk, T.4
  • 36
    • 33645844251 scopus 로고    scopus 로고
    • The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model
    • Luo W., Johnson A.W., Bentley D.L. The role of Rat1 in coupling mRNA 3'-end processing to transcription termination: implications for a unified allosteric-torpedo model. Genes Dev. 2006, 20:954-965.
    • (2006) Genes Dev. , vol.20 , pp. 954-965
    • Luo, W.1    Johnson, A.W.2    Bentley, D.L.3
  • 38
    • 84876963384 scopus 로고    scopus 로고
    • Definition of RNA polymerase II CoTC terminator elements in the human genome
    • Nojima T., Dienstbier M., Murphy S., Proudfoot N.J., Dye M.J. Definition of RNA polymerase II CoTC terminator elements in the human genome. Cell Rep. 2013, 3:1080-1092.
    • (2013) Cell Rep. , vol.3 , pp. 1080-1092
    • Nojima, T.1    Dienstbier, M.2    Murphy, S.3    Proudfoot, N.J.4    Dye, M.J.5
  • 41
    • 84937597324 scopus 로고    scopus 로고
    • Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1
    • Park J., Kang M., Kim M. Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1. Nucleic Acids Res. 2015, 43:2625-2637.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 2625-2637
    • Park, J.1    Kang, M.2    Kim, M.3
  • 42
    • 84880048366 scopus 로고    scopus 로고
    • Dismantling promoter-driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1
    • Pearson E.L., Moore C.L. Dismantling promoter-driven RNA polymerase II transcription complexes in vitro by the termination factor Rat1. J. Biol. Chem. 2013, 288:19750-19759.
    • (2013) J. Biol. Chem. , vol.288 , pp. 19750-19759
    • Pearson, E.L.1    Moore, C.L.2
  • 43
    • 84880144255 scopus 로고    scopus 로고
    • A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast
    • Porrua O., Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat. Struct. Mol. Biol. 2013, 20:884-891.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 884-891
    • Porrua, O.1    Libri, D.2
  • 44
    • 66149187105 scopus 로고    scopus 로고
    • Transcription termination by nuclear RNA polymerases
    • Richard P., Manley J.L. Transcription termination by nuclear RNA polymerases. Genes Dev. 2009, 23:1247-1269.
    • (2009) Genes Dev. , vol.23 , pp. 1247-1269
    • Richard, P.1    Manley, J.L.2
  • 45
    • 70349779344 scopus 로고    scopus 로고
    • Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae
    • Rondón A.G., Mischo H.E., Kawauchi J., Proudfoot N.J. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol. Cell 2009, 36:88-98.
    • (2009) Mol. Cell , vol.36 , pp. 88-98
    • Rondón, A.G.1    Mischo, H.E.2    Kawauchi, J.3    Proudfoot, N.J.4
  • 46
    • 84908315092 scopus 로고    scopus 로고
    • Genome-wide mapping of yeast RNA polymerase II termination
    • Schaughency P., Merran J., Corden J.L. Genome-wide mapping of yeast RNA polymerase II termination. PLoS Genet. 2014, 10:e1004632.
    • (2014) PLoS Genet. , vol.10 , pp. e1004632
    • Schaughency, P.1    Merran, J.2    Corden, J.L.3
  • 47
    • 0034307172 scopus 로고    scopus 로고
    • Dynamic association of capping enzymes with transcribing RNA polymerase II
    • Schroeder S.C., Schwer B., Shuman S., Bentley D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 2000, 14:2435-2440.
    • (2000) Genes Dev. , vol.14 , pp. 2435-2440
    • Schroeder, S.C.1    Schwer, B.2    Shuman, S.3    Bentley, D.4
  • 49
    • 79959345878 scopus 로고    scopus 로고
    • Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination
    • Skourti-Stathaki K., Proudfoot N.J., Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol. Cell 2011, 42:794-805.
    • (2011) Mol. Cell , vol.42 , pp. 794-805
    • Skourti-Stathaki, K.1    Proudfoot, N.J.2    Gromak, N.3
  • 51
    • 84901855485 scopus 로고    scopus 로고
    • Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications
    • Veloso A., Kirkconnell K.S., Magnuson B., Biewen B., Paulsen M.T., Wilson T.E., Ljungman M. Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res. 2014, 24:896-905.
    • (2014) Genome Res. , vol.24 , pp. 896-905
    • Veloso, A.1    Kirkconnell, K.S.2    Magnuson, B.3    Biewen, B.4    Paulsen, M.T.5    Wilson, T.E.6    Ljungman, M.7
  • 54
    • 26944433047 scopus 로고    scopus 로고
    • E Pluribus Unum: 3' end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs
    • Weiner A.M. E Pluribus Unum: 3' end formation of polyadenylated mRNAs, histone mRNAs, and U snRNAs. Mol. Cell 2005, 20:168-170.
    • (2005) Mol. Cell , vol.20 , pp. 168-170
    • Weiner, A.M.1
  • 55
    • 9644308046 scopus 로고    scopus 로고
    • Human 5'--> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites
    • West S., Gromak N., Proudfoot N.J. Human 5'--> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 2004, 432:522-525.
    • (2004) Nature , vol.432 , pp. 522-525
    • West, S.1    Gromak, N.2    Proudfoot, N.J.3
  • 56
    • 40649095272 scopus 로고    scopus 로고
    • Molecular dissection of mammalian RNA polymerase II transcriptional termination
    • West S., Proudfoot N.J., Dye M.J. Molecular dissection of mammalian RNA polymerase II transcriptional termination. Mol. Cell 2008, 29:600-610.
    • (2008) Mol. Cell , vol.29 , pp. 600-610
    • West, S.1    Proudfoot, N.J.2    Dye, M.J.3
  • 57
    • 0022819015 scopus 로고
    • Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3' end processing in the human alpha 2 globin gene
    • Whitelaw E., Proudfoot N. Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3' end processing in the human alpha 2 globin gene. EMBO J. 1986, 5:2915-2922.
    • (1986) EMBO J. , vol.5 , pp. 2915-2922
    • Whitelaw, E.1    Proudfoot, N.2
  • 58
    • 75149119376 scopus 로고    scopus 로고
    • An unexpected ending: noncanonical 3' end processing mechanisms
    • Wilusz J.E., Spector D.L. An unexpected ending: noncanonical 3' end processing mechanisms. RNA 2010, 16:259-266.
    • (2010) RNA , vol.16 , pp. 259-266
    • Wilusz, J.E.1    Spector, D.L.2
  • 60
    • 29544441415 scopus 로고    scopus 로고
    • Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript
    • Zhang Z., Gilmour D.S. Pcf11 is a termination factor in Drosophila that dismantles the elongation complex by bridging the CTD of RNA polymerase II to the nascent transcript. Mol. Cell 2006, 21:65-74.
    • (2006) Mol. Cell , vol.21 , pp. 65-74
    • Zhang, Z.1    Gilmour, D.S.2
  • 61
    • 2542489173 scopus 로고    scopus 로고
    • Analysis of polymerase II elongation complexes by native gel electrophoresis. Evidence for a novel carboxyl-terminal domain-mediated termination mechanism
    • Zhang Z., Wu C.-H., Gilmour D.S. Analysis of polymerase II elongation complexes by native gel electrophoresis. Evidence for a novel carboxyl-terminal domain-mediated termination mechanism. J. Biol. Chem. 2004, 279:23223-23228.
    • (2004) J. Biol. Chem. , vol.279 , pp. 23223-23228
    • Zhang, Z.1    Wu, C.-H.2    Gilmour, D.S.3
  • 62
    • 84938741134 scopus 로고    scopus 로고
    • Poly(A) Signal-Dependent Transcription Termination Occurs through a Conformational Change Mechanism that Does Not Require Cleavage at the Poly(A) Site
    • Zhang H., Rigo F., Martinson H.G. Poly(A) Signal-Dependent Transcription Termination Occurs through a Conformational Change Mechanism that Does Not Require Cleavage at the Poly(A) Site. Mol. Cell 2015, 59:437-448.
    • (2015) Mol. Cell , vol.59 , pp. 437-448
    • Zhang, H.1    Rigo, F.2    Martinson, H.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.